User: raf4

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raf410
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Posts by raf4

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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... Steve and Gordon, I have since found out that the count  files were indeed produced by the sequencing core here using different alignment algorithms and different assemblies (gtf files)! I have suggested that the investigator whom I am helping ask the core to realign the older read data with the ne ...
written 9 days ago by raf410
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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... Steve and Gordon, Thank you for your answers. I just remembered that the first batch was mapped to ENSEMBL and then translated to NCBI gene symbols. The second was mapped NCBI genes. That must be the problem. I will analyze them in a compatible way henceforth. If batch corrections are necessary, I ...
written 19 days ago by raf410 • updated 18 days ago by Gordon Smyth30k
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Comment: A: Subject: Strange glitch in Voom curve resulting from batch effects
... Steve, Most of the genes were the same. I forget the number of NAs but I can check. fewer than 1,000 I think. There are 5 replicates of one condition in the old batch and 5 replicates each for 4 conditions in the new batch. The filter I used for low expressing genes is: isexpr<-rowSums(cpm(y) ...
written 20 days ago by raf410 • updated 19 days ago by Gordon Smyth30k
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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... Steve, Thank you for our immediate reply. As far as I know, "Yes", because it was done with the same protocol at the same core. However, I will query the experimentalist directly. Best wishes, Rich     ...
written 20 days ago by raf410
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Subject: Strange glitch in Voom curve resulting from batch effects
... Dear Bioconductor List, I am analyzing an RNAseq experiment taken from two different batches. I have encountered a strange voom plot and cannot get rid of it by taking batch effects into account as a co-variate. I will present the relevant information, and then ask some questions at the end. All i ...
batcheffect limma voom covariate written 20 days ago by raf410 • updated 18 days ago by Gordon Smyth30k
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Rsubread crash on Mac during alignment
... Dear Bioconductor Forum, Rsubread crashed on my 32Gb Mac on a particular pair of fastq files. It worked fine on the previous file in the dataset and also other times I had used it. The CPU was at 100% and the memory was at 24.3% all the way through the run. The script was library(Rsubread) align( ...
rsubread software error written 3 months ago by raf410 • updated 9 weeks ago by Wei Shi2.6k
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Normalization and batch effect adjustment of fluidgm pcr data to be analyzed with Limma
... Dear all, Does fluidgm qt-pcr data which has normalized against a reference gene (eg GAPDH) on each plate have to be normalized further within and between plates. If so, How does one know which method to use (quantile, cyclic loess) etc. The data is to be analyzed with Limma. Thanks and best wis ...
normalization limma fluidigm pcr written 4 months ago by raf410 • updated 4 months ago by Gordon Smyth30k
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Error message in Rsubread detectionCall command
... Dear Bioconductor users and (I hope) Rsubread developers, I have the following error message using the detectionCall command on Rsubread run on a Mac:   ################################################################ R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" Copyright (C) 2015 The ...
rsubread written 15 months ago by raf410

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